Starting phenix.real_space_refine on Sat Mar 16 07:09:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/03_2024/8osk_17157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/03_2024/8osk_17157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/03_2024/8osk_17157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/03_2024/8osk_17157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/03_2024/8osk_17157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osk_17157/03_2024/8osk_17157.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.951 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 14 5.16 5 C 7941 2.51 5 N 2662 2.21 5 O 3130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13995 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2520 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2564 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1591 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 1068 Unresolved non-hydrogen angles: 1365 Unresolved non-hydrogen dihedrals: 909 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 13, 'TYR:plan': 16, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 18, 'GLU:plan': 28, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 631 Chain: "N" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1427 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 4 Unresolved non-hydrogen bonds: 915 Unresolved non-hydrogen angles: 1154 Unresolved non-hydrogen dihedrals: 771 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 16, 'GLU:plan': 14, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 517 Time building chain proxies: 7.75, per 1000 atoms: 0.55 Number of scatterers: 13995 At special positions: 0 Unit cell: (142.805, 145.34, 122.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 248 15.00 O 3130 8.00 N 2662 7.00 C 7941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.76 Conformation dependent library (CDL) restraints added in 1.9 seconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 60.6% alpha, 14.7% beta 124 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'M' and resid 34 through 60 removed outlier: 3.873A pdb=" N MET M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 90 Processing helix chain 'M' and resid 108 through 118 Processing helix chain 'M' and resid 136 through 143 removed outlier: 4.123A pdb=" N SER M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 150 Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 159 through 161 No H-bonds generated for 'chain 'M' and resid 159 through 161' Processing helix chain 'M' and resid 162 through 173 removed outlier: 3.568A pdb=" N VAL M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS M 173 " --> pdb=" O ILE M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 186 Processing helix chain 'M' and resid 293 through 298 Processing helix chain 'M' and resid 300 through 305 removed outlier: 3.531A pdb=" N VAL M 304 " --> pdb=" O LEU M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 313 Processing helix chain 'M' and resid 316 through 332 removed outlier: 4.156A pdb=" N ASN M 320 " --> pdb=" O ASP M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 384 removed outlier: 3.675A pdb=" N GLU M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 105 removed outlier: 3.663A pdb=" N LEU N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 112 Processing helix chain 'N' and resid 117 through 129 Processing helix chain 'N' and resid 151 through 160 Processing helix chain 'N' and resid 182 through 187 removed outlier: 3.519A pdb=" N ILE N 186 " --> pdb=" O SER N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 195 Processing helix chain 'N' and resid 198 through 202 Processing helix chain 'N' and resid 204 through 215 removed outlier: 4.228A pdb=" N ALA N 209 " --> pdb=" O PRO N 205 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS N 210 " --> pdb=" O LYS N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 249 No H-bonds generated for 'chain 'N' and resid 247 through 249' Processing helix chain 'N' and resid 360 through 368 removed outlier: 3.601A pdb=" N THR N 364 " --> pdb=" O ASP N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 375 Processing helix chain 'N' and resid 378 through 382 Processing helix chain 'N' and resid 384 through 399 removed outlier: 4.237A pdb=" N GLY N 389 " --> pdb=" O GLN N 385 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N HIS N 390 " --> pdb=" O ASP N 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.006A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.214A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.886A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.398A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 131 through 134 removed outlier: 6.299A pdb=" N ILE M 131 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET M 126 " --> pdb=" O ILE M 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 264 through 266 removed outlier: 4.105A pdb=" N TRP M 350 " --> pdb=" O MET M 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 286 through 289 removed outlier: 6.129A pdb=" N ARG M 279 " --> pdb=" O LEU M 287 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU M 289 " --> pdb=" O THR M 277 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR M 277 " --> pdb=" O LEU M 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 176 through 179 removed outlier: 6.440A pdb=" N VAL N 168 " --> pdb=" O LEU N 177 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL N 179 " --> pdb=" O LEU N 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU N 166 " --> pdb=" O VAL N 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 356 through 359 removed outlier: 6.523A pdb=" N ARG N 349 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL N 359 " --> pdb=" O VAL N 347 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL N 347 " --> pdb=" O VAL N 359 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR N 439 " --> pdb=" O PHE N 429 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 356 through 359 removed outlier: 6.523A pdb=" N ARG N 349 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL N 359 " --> pdb=" O VAL N 347 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL N 347 " --> pdb=" O VAL N 359 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR N 439 " --> pdb=" O PHE N 429 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2076 1.32 - 1.44: 4751 1.44 - 1.57: 7353 1.57 - 1.69: 496 1.69 - 1.82: 24 Bond restraints: 14700 Sorted by residual: bond pdb=" NE ARG H 31 " pdb=" CZ ARG H 31 " ideal model delta sigma weight residual 1.326 1.366 -0.040 1.10e-02 8.26e+03 1.34e+01 bond pdb=" CA PRO M 294 " pdb=" C PRO M 294 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.20e+00 bond pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.41e+00 bond pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.40e+00 bond pdb=" NE ARG F 40 " pdb=" CZ ARG F 40 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.35e+00 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.51: 1376 105.51 - 112.32: 7841 112.32 - 119.13: 3951 119.13 - 125.93: 7111 125.93 - 132.74: 767 Bond angle restraints: 21046 Sorted by residual: angle pdb=" C LEU D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 angle pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta sigma weight residual 119.56 126.95 -7.39 1.02e+00 9.61e-01 5.25e+01 angle pdb=" C ASP M 203 " pdb=" N PRO M 204 " pdb=" CA PRO M 204 " ideal model delta sigma weight residual 119.87 127.29 -7.42 1.04e+00 9.25e-01 5.08e+01 angle pdb=" C VAL N 331 " pdb=" N PRO N 332 " pdb=" CA PRO N 332 " ideal model delta sigma weight residual 120.03 127.07 -7.04 9.90e-01 1.02e+00 5.06e+01 angle pdb=" C LEU H 102 " pdb=" N PRO H 103 " pdb=" CA PRO H 103 " ideal model delta sigma weight residual 119.78 127.01 -7.23 1.03e+00 9.43e-01 4.93e+01 ... (remaining 21041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 7173 35.90 - 71.80: 998 71.80 - 107.70: 13 107.70 - 143.60: 0 143.60 - 179.49: 2 Dihedral angle restraints: 8186 sinusoidal: 4293 harmonic: 3893 Sorted by residual: dihedral pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sinusoidal sigma weight residual 220.00 40.51 179.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 133 " pdb=" C3' DG I 133 " pdb=" O3' DG I 133 " pdb=" P DT I 134 " ideal model delta sinusoidal sigma weight residual 220.00 58.70 161.30 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA LEU H 102 " pdb=" C LEU H 102 " pdb=" N PRO H 103 " pdb=" CA PRO H 103 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1673 0.052 - 0.103: 583 0.103 - 0.155: 215 0.155 - 0.206: 19 0.206 - 0.258: 4 Chirality restraints: 2494 Sorted by residual: chirality pdb=" CG LEU F 22 " pdb=" CB LEU F 22 " pdb=" CD1 LEU F 22 " pdb=" CD2 LEU F 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" P DC I 23 " pdb=" OP1 DC I 23 " pdb=" OP2 DC I 23 " pdb=" O5' DC I 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.57 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2491 not shown) Planarity restraints: 1881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 34 " 0.106 2.00e-02 2.50e+03 4.63e-02 6.43e+01 pdb=" N9 DG I 34 " -0.006 2.00e-02 2.50e+03 pdb=" C8 DG I 34 " -0.031 2.00e-02 2.50e+03 pdb=" N7 DG I 34 " -0.045 2.00e-02 2.50e+03 pdb=" C5 DG I 34 " -0.042 2.00e-02 2.50e+03 pdb=" C6 DG I 34 " 0.011 2.00e-02 2.50e+03 pdb=" O6 DG I 34 " 0.079 2.00e-02 2.50e+03 pdb=" N1 DG I 34 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DG I 34 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG I 34 " -0.020 2.00e-02 2.50e+03 pdb=" N3 DG I 34 " -0.027 2.00e-02 2.50e+03 pdb=" C4 DG I 34 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " 0.093 2.00e-02 2.50e+03 4.22e-02 4.89e+01 pdb=" N9 DA I 120 " -0.005 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " -0.019 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " -0.035 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " -0.038 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " -0.032 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 111 " 0.090 2.00e-02 2.50e+03 4.53e-02 4.61e+01 pdb=" N1 DC I 111 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC I 111 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 111 " -0.046 2.00e-02 2.50e+03 pdb=" N3 DC I 111 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 111 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC I 111 " 0.063 2.00e-02 2.50e+03 pdb=" C5 DC I 111 " -0.046 2.00e-02 2.50e+03 pdb=" C6 DC I 111 " -0.043 2.00e-02 2.50e+03 ... (remaining 1878 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3091 2.79 - 3.32: 12704 3.32 - 3.85: 26282 3.85 - 4.37: 30601 4.37 - 4.90: 43872 Nonbonded interactions: 116550 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.263 2.440 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.418 2.520 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 35 " model vdw 2.500 2.520 nonbonded pdb=" OG SER G 40 " pdb=" O SER H 87 " model vdw 2.516 2.440 nonbonded pdb=" N GLN F 27 " pdb=" OE1 GLN F 27 " model vdw 2.519 2.520 ... (remaining 116545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 124) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.86 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.200 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 45.080 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 14700 Z= 0.531 Angle : 1.122 7.874 21046 Z= 0.762 Chirality : 0.058 0.258 2494 Planarity : 0.008 0.053 1881 Dihedral : 24.393 179.494 5650 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1311 helix: 1.37 (0.18), residues: 740 sheet: 0.95 (0.43), residues: 135 loop : 1.25 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.003 0.001 HIS H 49 PHE 0.009 0.001 PHE D 70 TYR 0.030 0.004 TYR C 57 ARG 0.007 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 PHE cc_start: 0.8213 (m-80) cc_final: 0.7984 (m-10) REVERT: E 99 TYR cc_start: 0.8842 (t80) cc_final: 0.8498 (t80) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2793 time to fit residues: 127.1304 Evaluate side-chains 216 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 14700 Z= 0.360 Angle : 0.727 12.528 21046 Z= 0.421 Chirality : 0.043 0.157 2494 Planarity : 0.005 0.041 1881 Dihedral : 28.147 179.269 4122 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.04 % Allowed : 15.81 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.22), residues: 1311 helix: 1.65 (0.18), residues: 765 sheet: 0.72 (0.44), residues: 129 loop : 1.05 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.010 0.002 HIS B 75 PHE 0.016 0.002 PHE B 100 TYR 0.024 0.002 TYR B 88 ARG 0.010 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 237 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.8896 (m-80) cc_final: 0.8695 (m-80) REVERT: D 99 ARG cc_start: 0.9500 (mtp85) cc_final: 0.9100 (mtp85) REVERT: F 46 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8863 (pt) outliers start: 45 outliers final: 25 residues processed: 255 average time/residue: 0.2546 time to fit residues: 94.4344 Evaluate side-chains 230 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 50.0000 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 0.0060 chunk 139 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 40.0000 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 108 ASN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14700 Z= 0.274 Angle : 0.656 9.883 21046 Z= 0.381 Chirality : 0.040 0.174 2494 Planarity : 0.004 0.061 1881 Dihedral : 28.416 179.282 4122 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.38 % Allowed : 18.15 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1311 helix: 1.81 (0.18), residues: 764 sheet: 0.60 (0.44), residues: 129 loop : 0.84 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 PHE 0.015 0.002 PHE E 104 TYR 0.033 0.002 TYR B 88 ARG 0.005 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 239 average time/residue: 0.2373 time to fit residues: 83.6270 Evaluate side-chains 204 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 50.0000 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 149 optimal weight: 30.0000 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14700 Z= 0.221 Angle : 0.626 13.226 21046 Z= 0.364 Chirality : 0.039 0.166 2494 Planarity : 0.004 0.058 1881 Dihedral : 28.227 178.612 4122 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.91 % Allowed : 22.54 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.23), residues: 1311 helix: 1.91 (0.19), residues: 761 sheet: 0.56 (0.44), residues: 129 loop : 0.74 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.009 0.001 HIS F 75 PHE 0.010 0.001 PHE B 100 TYR 0.032 0.002 TYR A 54 ARG 0.003 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LEU cc_start: 0.7120 (mt) cc_final: 0.6607 (mt) outliers start: 25 outliers final: 13 residues processed: 222 average time/residue: 0.2323 time to fit residues: 77.0528 Evaluate side-chains 205 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 14700 Z= 0.394 Angle : 0.711 12.852 21046 Z= 0.411 Chirality : 0.043 0.212 2494 Planarity : 0.005 0.054 1881 Dihedral : 28.835 179.547 4122 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.01 % Allowed : 25.82 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1311 helix: 1.56 (0.19), residues: 762 sheet: 0.36 (0.43), residues: 140 loop : 0.68 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.010 0.001 HIS F 75 PHE 0.015 0.002 PHE D 65 TYR 0.035 0.003 TYR B 98 ARG 0.004 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 203 average time/residue: 0.2242 time to fit residues: 69.6056 Evaluate side-chains 201 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14700 Z= 0.200 Angle : 0.630 9.693 21046 Z= 0.362 Chirality : 0.038 0.171 2494 Planarity : 0.004 0.057 1881 Dihedral : 28.392 177.277 4122 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.66 % Allowed : 29.58 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1311 helix: 1.82 (0.19), residues: 761 sheet: 0.49 (0.44), residues: 140 loop : 0.67 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.001 PHE D 65 TYR 0.038 0.002 TYR B 88 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 ASN cc_start: 0.8853 (t0) cc_final: 0.8504 (t0) outliers start: 17 outliers final: 13 residues processed: 212 average time/residue: 0.2199 time to fit residues: 71.5857 Evaluate side-chains 200 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 14700 Z= 0.361 Angle : 0.687 9.982 21046 Z= 0.396 Chirality : 0.041 0.222 2494 Planarity : 0.005 0.062 1881 Dihedral : 28.667 179.791 4122 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.38 % Allowed : 28.01 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1311 helix: 1.64 (0.19), residues: 762 sheet: 0.36 (0.44), residues: 140 loop : 0.61 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 PHE 0.011 0.002 PHE C 25 TYR 0.034 0.002 TYR B 88 ARG 0.005 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 193 average time/residue: 0.2146 time to fit residues: 63.8117 Evaluate side-chains 197 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 50.0000 chunk 135 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 14700 Z= 0.358 Angle : 0.705 11.383 21046 Z= 0.406 Chirality : 0.042 0.208 2494 Planarity : 0.005 0.058 1881 Dihedral : 28.931 177.979 4122 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.38 % Allowed : 28.48 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.23), residues: 1311 helix: 1.57 (0.19), residues: 751 sheet: 0.10 (0.46), residues: 131 loop : 0.58 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 PHE 0.021 0.002 PHE E 104 TYR 0.023 0.002 TYR A 99 ARG 0.004 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.8918 (m-80) cc_final: 0.8675 (m-80) outliers start: 28 outliers final: 23 residues processed: 196 average time/residue: 0.2260 time to fit residues: 67.2747 Evaluate side-chains 199 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 91 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14700 Z= 0.301 Angle : 0.696 15.845 21046 Z= 0.395 Chirality : 0.041 0.236 2494 Planarity : 0.004 0.058 1881 Dihedral : 28.838 177.002 4122 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.44 % Allowed : 29.89 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1311 helix: 1.64 (0.19), residues: 752 sheet: -0.01 (0.46), residues: 131 loop : 0.60 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 PHE 0.015 0.002 PHE B 61 TYR 0.025 0.002 TYR A 99 ARG 0.005 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 20 residues processed: 195 average time/residue: 0.2121 time to fit residues: 63.5807 Evaluate side-chains 193 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14700 Z= 0.276 Angle : 0.694 15.750 21046 Z= 0.394 Chirality : 0.041 0.273 2494 Planarity : 0.004 0.057 1881 Dihedral : 28.725 176.779 4122 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.50 % Allowed : 31.77 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1311 helix: 1.62 (0.19), residues: 757 sheet: 0.01 (0.47), residues: 131 loop : 0.57 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.008 0.001 HIS F 75 PHE 0.015 0.002 PHE B 61 TYR 0.020 0.002 TYR G 57 ARG 0.005 0.000 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 192 average time/residue: 0.2143 time to fit residues: 63.1047 Evaluate side-chains 196 residues out of total 1169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 40.0000 chunk 51 optimal weight: 0.0980 chunk 126 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.075227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.053762 restraints weight = 126707.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.053957 restraints weight = 67323.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.054486 restraints weight = 40917.077| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 14700 Z= 0.282 Angle : 0.701 15.148 21046 Z= 0.397 Chirality : 0.041 0.232 2494 Planarity : 0.004 0.054 1881 Dihedral : 28.701 176.984 4122 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.19 % Allowed : 31.61 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1311 helix: 1.55 (0.19), residues: 766 sheet: -0.08 (0.44), residues: 140 loop : 0.63 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 284 HIS 0.007 0.001 HIS F 75 PHE 0.034 0.002 PHE B 61 TYR 0.021 0.002 TYR A 99 ARG 0.004 0.000 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2708.97 seconds wall clock time: 48 minutes 51.96 seconds (2931.96 seconds total)